It is raining in the Mopti region in central Mali and most of the fields are filled with millet and rice seedlings, turning the usually dusty landscape a vivid green. But interspersed with these are vast tracts of land that lie uncultivated because farmers could not get the seeds to plant in them.

The government estimates rice production this year could be reduced by 20% to 30% as a result, according to USAid's famine early warning systems network, Fews Net.

"This will have several dimensions: production will go down, farmers will be left more food-insecure and they won't have enough seed to plant next year," said an international donor active in agriculture in Mali, who estimates that hundreds of hectares of land in Mopti will not bear crops this year because of seed shortages.

The cycle of drought and seed shortages, aggravated by political instability in northern Mali and a flow of refugees, has had devastating effects in Mopti. Pockets of severe drought in 2011-12 left only 11% of households with enough seed to plant in this year's season, the donor suggested. The closing of banks in Mopti to protect them from looters from the north has squeezed farmers' access to credit to buy seeds.

Most farmers produced enough grain in 2011 to last only five or six months, said Chery Traoré, agriculture programme manager at Catholic Relief Services (CRS), leaving them with no seeds for planting because they had all been eaten. As a result, they were forced to buy seed on the market.

There is still a little time left to plant – Traoré says mid-August is probably the latest farmers can plant, but that is risky because millet and rice take several months to grow and the duration of the rains is uncertain.

Farmers who managed to get seed to plant were positive about the rains so far, but still worried. IRIN spoke to two of them just outside Sévaré, in the Mopti region. "We need these rains to last through August. If we can get good rains throughout, we may be OK this year," said Moussa Touré. Mamadou Bodou, a father of 12, said: "I planted just one field this year – I can't even pay off my debts with that – it will get me nowhere." He pointed at the empty fields all around, stretching into the distance.

According to Fews Net, the areas most affected by severe rice shortages are the agro-pastoral (mainly rice-growing) parts of the Mopti region, which stretch north all the way to Timbuktu, and the inner Niger Delta zone, which relies on flood-based rice cultivation. The network predicts an average harvest in most of the rest of the country, but warns that a shortened rainy season and possible locust infestation would undermine the harvest. Sightings of adult locusts have been reported in the Tamesna and Adrar areas of Kidal in northern Mali since May, but insecurity has limited access to evaluate the situation.

It is difficult to estimate the seed shortage across the country, but it could be as much as 50%, said Maguette Ndiaye, emergency co-ordinator at the UN Food and Agriculture Organisation (FAO). CRS ran several large seed fairs in the Mopti region in the runup to planting. They gave farmers vouchers to exchange for seeds in the market and found an "enormous demand", said the NGO's head, Timothy Bishop.

Critics say donors should have done more to foresee projected shortages and distribute seeds early. The EU has not done enough, said one NGO; another said the FAO did not present the needs in enough detail, but noted that it is severely underfunded this year. Ndiaye said the FAO has only $4m of the $10m it needs to help Mali's agriculture, fishing and livestock sectors, while its regional head, José Luis Fernandez, has stressed the severe shortage of funds for agricultural and livestock programmes throughout the Sahel.

Donor pullout

The agriculture minister, Moussa Sidibé, says donors have put funding and projects on hold because of the political situation, which has hit the agricultural sector hard and will inevitably impact on this year's harvest. "The donor pullout has severely affected us," Sidibé told IRIN. "Up to 190bn CFA [$356,000] worth of projects has been stopped … donors should not throw the baby out with the bathwater."

Many granaries in Mopti were empty at the start of planting season. Dozens of agriculture programmes have been affected, including seed fairs, microfinance for farmers, access to credit for fertilisers and seeds, training programmes, and assistance with rainfall monitoring and new seed varieties.

A USAid-funded programme for CRS, which helps 47,000 farmers across Mopti, Gao and Douentza with micro-finance loans to buy seed and fertilisers, and create a value chain for their products, has been stopped, said Chery Traoré. "Without donor aid it's unclear if the government will even be able to assess the harvest this year," Gaoussou Traoré, head of programmes in the accelerated growth team at USAid, said.

On top of this, farmers face countrywide fertiliser shortages as suppliers have been reluctant to sell on credit because loans from last year were not sufficiently repaid, said Mary Diallo, co-ordinator of the government's early warning system.

In most years, the agriculture ministry subsidises fertiliser prices in some areas, but funding shortages and insecurity in the north have stopped it from doing so extensively this year, said Sidibé. The ministry and German aid agency GTZ, which funds agricultural associations directly, are working with other agriculture donors to see if they can start doing the same.

FAO's Ndiaye stressed that although severe shortages remain, agencies have been doing what they can – the FAO provided seeds to 3,000 farmers in Kayes, the agricultural region in western Mali; it distributed rice seeds in the north through Handicap International and other NGOs, and it helped rice farmers by irrigating their fields.